The Truth Is Harder to Digest Overall
by Pittoo Sassy Angel of Darkness
Summary: A strange man, reunited with a childhood friend, and Team Aqua's fight with Team Magma... This is Emerald's new life in Hoenn as he begins his journey alongside the happy go lucky Ruby. Secretly, he wonders if there is a deep, underlayed meaning to all of these odd happenings and is determined to solve this mystery with his new friends in this, truth really is harder to digest...
1. Emerald's Battle Flair

_**The Truth is Harder to Digest Overall**_

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 **Author's Note:**

 **This is an idea I have been sitting on for a while thanks to my girlfriend. In Pokémon Emerald, there is this man named Scott who seemingly follows you around like a stalker in between stalking other Trainers. This explores the possibility of his motives being rather different with the prestigious Battle Frontier being his final domain where he reveals his true plans to the ones who are given the title, World's Best Pokémon Trainer. Just sit back and enjoy the ride. Here we go! Oh. Sorry for all those formatting errors before. I hope this fixed them all, ad if not, I apologize and will try again.**

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 **Episode 1 - Emerald's Battle Flair**

Riding with their belongings in the moving van sure was tiring for the boy, though, it was his mother's idea, so why complain? The answer: he wasn't. However, he felt like he was going to fall asleep from boredom. There really was nothing he wanted to do in there. Finally, he felt the vehicle come to a stop and the door opened to reveal the front of a house. They had arrived. He stepped down and put an arm above his eyes to block the sun which filtered through a tree canopy, so normally there would be no need for him to do so, but his eyes were used to the darkness inside the van. He had to adjust... "Emerald! Welcome to Littleroot Town!" greeted his mother as she led him inside. "The movers' Pokémon do all the work, so it's very relaxing."

". . . . ." He said nothing as he watched three monkey Pokémon with red hair and white fur unpack and install or place everything where it needed to be. ' _These Vigroth do all the heavy lifting while their companions get to take it easy. The movers should be helping their Pokémon, not sitting back and drinking coffee. And... Mom's alright with this? Ugh..._ ' "You should go check and make sure your things are put away correctly!" she said as she pushed him to the stairwell. "Oh. I almost forgot! Dad bought you a new clock to mark the move here. Don't forget to set and start it! Your room is the last door on the left! Go on, honey."

"Fine," the boy in the white hat responded simply as he ascended the stairs. Once in his room, he sat down on his bed with a sigh. He missed his old life back in Kanto... all of the friends he had to leave behind, just so that his father could be closer to home. Even still, the gym his dad was the gym leader of was two towns over. It wasn't too far, but it was a walk from there to home and back. How Emerald wished he could make his father proud by becoming a great Pokémon Trainer... but... he didn't have a Pokémon of his own... or a friend in the world. He felt lonely. He looked around his room again and noticed the blue wall clock. I should set it... he thought as he stood and walked over to it, taking it down and turning the dial on the back until it read 2:48 PM. Once that was done, he hung it back up and walked over to his desk where his computer was. He booted it up, not really expecting anything, but when it got to the desktop, a Pidgeotto flapped its way across with an email in its talons. He raised an eyebrow as he clicked on the bird's feet to make it drop the letter which opened automatically. It was from one of his old friends. ' _Heh... Thank you, Red... It's nice to know you miss me..._ ' he thought as he read over it. No sooner had he finished reading than his mother walked into the room with a smile. "The movers are all done and have left. Come on downstairs when you're ready." In reply, he nodded once, shutting down his PC and carefully closing his bedroom door before following his mom down the stairs and across the house into the living room. "One of Dad's friends lives in town. Professor Birch, I believe. He lives next door. Why don't you go introduce yourself?" she suggested after sitting at the table.

". . . . ." Again, he said nothing, only nodding in agreement as he walked out the door. ' _Oh, Emerald... You've barely said a word since your father requested we move here..._ ' thought the protagonist's mom as she stared at a picture on the wall of her son and his best friend, Red. I hope he makes some new friends here in Hoenn...

Outside, he could hear the calls of several different Pokémon as he walked to Professor Birch's house and knocked against the door a couple times. A few moments later, a blonde woman answered and looked at him in question. "Hello... and... you are?" Rather than give a long explanation, he spoke only his name. "Oh! So you're Emerald! We have a daughter the same age as you! She was thrilled about making a new friend! Our daughter is upstairs... I think..." she said as she beckoned him inside and led him to the stairs which he stepped up on. Finding the girl's room was easy enough, so he knocked on the door and waited for a minute before a voice spoke from behind him. "Hi! You must be Emerald! Pleased to meet you! I'm Ruby! Oh, I really wanted to meet you! I was hoping we could be friends! Hm? Emerald... don't you have a Pokémon?" She had glanced at his belt and noticed not a single PokéBall lay clamped on it.

". . . . .No," he admitted in a rather awkward manner.

"Don't be nervous! We are friends, now, after all! Say, do you want me to catch you one? Oh, no! I'm sorry, Emerald! I was supposed to be helping my dad catch some Pokémon for his research! But I promise, I'll catch you one later!" And with that, she left, her brunette hair bouncing as she rushed. After a few seconds of standing still, lost in thought, Emerald left Ruby's house and heard... shouting...? He ran to the source of the noise, the seams in his shoes popping as they weren't meant for the force running caused on them. "There's something happening down the road here, but I'm too small to go check it out. Will you go see what it is for me?" begged a small little girl to him as he approached. With a nod, he went into Route 101 where he witnessed a man in a lab coat running for his life as an enraged Zigzagoon chased him.

"Help me! Hey! You! Over there, quick! In my bag, there's a PokéBall!" the man yelled. In a flash, the boy went to the bag and grabbed the center red and white, metal ball, throwing it out to reveal a small, orange and yellow chick. "Torchic! Use scratch!" he called to the basic form starter Pokémon, a bit surprised when she obeyed him. After two scratches, the tiny raccoon Pokémon fainted, leaving Torchic and Emerald as the victors.

"Thank you. I was studying wild Pokémon in their habitats when that one jumped." The man looked him up and down for a second before saying, "You're Emerald. Hmm. Come by my laboratory later. I'll be expecting you."

'Everyone _seems to be in such a rush... Uh! He forgot Torchic! I still have her... I'll return her when I stop by in a while..._ ' thought the blackette in the hat as he looked at the little creature at his side which stared back with a fierce intensity that was shocking for something so cute. "Let's give you back to your owner..." he sighed, already beginning to like the monster. If he wasn't mistaken, he could have sworn the small Pokémon gave him a look of sorrow at that. Was it possible that she was starting to take a liking to him as well? Rather than ponder something that would without a doubt upset him, he began walking back to Littleroot Town. Every so often, he'd glance at his heels where, sure enough, Torchic kept up with his pace, making adorable noises and looking back with pleading eyes. Finally, he reached the lab where the plaque read, "Prof. Birch's Pokémon Research Center." He sighed again as he turned the door knob and proceeded inside with the animal.

"Ah, Emerald!" called the man whom he now knew to be the esteemed Pokémon Professor, Birch. "I knew you'd swing by. Your father was a bit concerned that you weren't ready to start your Pokémon journey, but after seeing you battle earlier and pull it off with a bomb, I can say without an inch of doubt that your father's blood runs in your veins with skill that could be unrivaled. So, I will give you the Pokémon you battled beside earlier." At this, Emerald's eyes lit up, as did Torchic's. "While you're at it, why don't you give a nickname to that Pokémon?"

The boy gazed at his new companion as he thought of a fitting name for her. It had to be something she would like as well... "Torchic... how does Flair sound to you as a name...?" he inquired of her as he knelt so that he could be more on level with the Pokémon. "Torchic!" she squealed in delight as she jumped into his arms, her adorable eyes shining.

"Flair it is. If you work with that Pokémon, I'm sure the two of you could become a fantastic team. Which reminds me! My kid, Ruby is out on Route 103 helping me with my research. Emerald, why don't you go and meet her? Have her teach you what it means to be a Pokémon Trainer?"

"...Sure..." he responded simply as he stood, his new-found friend in his arms.

"Excellent! I'm sure Ruby will be happy, too!"

With a nod, the newbie Trainer left, his destination being Route 103 where supposedly the girl he'd met earlier that day was. On the way, he passed through Odale Town which was also a very small community, but the only differences from Littleroot Town it had were a PokeMart and a Pokémon Center. He smiled down at his Torchic who was still in his arms, trilling happily, as he walked. Once he arrived at the designated area, he spotted her immediately. She was focused on her project, jotting down notes in a notebook. He went over to her and tapped her on the shoulder.

"Okay... so the Pokémon found on Route 103 include- huh? Oh! Emerald! Aww... you have a Pokémon now! She's so cute. Hey, you wanna battle? I can show you my Pokémon!" she stated.

"Mmn..." he grunted with a nod. "Bring it on, Ruby!" ' _Why am I talking so much lately...? I... I don't understand..._ '

"Alrighty! But just because you're a newbie, that doesn't mean I'm going to hold anything back!" cheered Ruby as she threw out her PokéBall. "Go! Skippy!" In front of her, a Mudkip appeared in a flash of light.

"Flair! You're up!" he yelled as he placed his Torchic on the ground, watching her get into a battle stance.

"Mudkip, kip kip!"

"Torchic torchi!" With their cries, the two Pokémon leaped into action, a fierce fight slowly began.

"Skippy! Tackle Attack!"

"Flair! Use scratch!" The two creatures did as they were bidden, their attacks colliding. The fight lasted for quite some time, both opponents equally and skillfully matched, but, in the end, Emerald's Torchic was victorious as it wobbled slightly, staying up during Ruby's Mudkip's ten count.

"Wow, Emerald... you're pretty good!" she complimented as she pulled her Pokémon into her arms and used a potion on it. "I think I see why my dad has his eye on you now. I mean, your Pokémon already likes you and you only just got it. I think you'll be able to befriend any Pokémon with ease. Well, I'm heading back to my dad's lab. You wanna tag along?"

Before even trying to answer, Emerald picked up his Pokémon and looked her over to be sure she was alright before saying, "Fine..." With that, the friends headed back to the Pokémon Lab where Professor Birch was waiting. They explained the battle, Ruby doing more of the talking rather than Emerald. Once their tale had been told, the professor laughed with joy. "Brilliant! Absolutely brilliant! Oh! Reminds me! I have something I want to give you, Emerald!" he said as he gave him a PokéDex.

"Yay! You have a PokéDex, too! Then, here! I'll give you five PokéBalls!" said Ruby as she did just that. "Oh, Dad? I want to join Emerald on his Pokémon journey! May I?"

"Yes. I would much rather you two go as a team, that is... if it's alright with Emerald."

"Please, Emerald?"

He thought for a minute before responding with a nod of agreement. "Oh, thank you, Emerald! You won't regret it!" she cheered as she gave him a quick hug, her color flushed darkly, and she let him go in embarrassment to which he raised a curious eyebrow and his Torchic growled in a way that was meant to be menacing but really was too adorable to be any of the sort. Emerald, on the other hand, looked at the girl in red as a thought process wound its way through his mind. What is she so embarrassed about...? And... what was with Flair's protective response? All that happened to be was a friendly gesture, correct? So why?

And that is how Emerald and Ruby began their journey across the Hoenn Region as two unlikely friends in the beginning with a common goal. Emerald was glad he wouldn't be traveling alone, and was shocked that before they could even leave, his mom gave him a pair of Running Shoes as well as a bag containing several changes of clothes, assorted items, and Poké Cash as she saw them off with a small smile, Ruby's mother doing the exact same thing. It was pure luck the two didn't look back, otherwise, they would have seen their mothers crying as their babies left home to begin their adventure through the land, showing they had grown up and didn't necessarily need fussing over. The moment was heartfelt as the women watched their oldest children head off, not knowing when they would see them again...


	2. Norman, the Frail Boy, and the Stranger

_**The Truth is Harder to Digest Overall**_

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 **Episode 2 - Norman, the Frail Boy, and the Stranger in Petalburg City**

A few Pokémon battles and a couple hours later, Ruby and Emerald arrived in Petalburg City, tired and ready to turn in for the night. "The Pokémon Center should allow us overnight lodging..."

"...Then... I see no reason we shouldn't go there and rest up. About how much are we looking at in cost?" questioned Emerald as he looked at his partner on this long journey ahead of them.

"I think it's 100 Poké a night and we definitely have more than that thanks to those random Trainer battles back there on Route 102!"

". . . ." He had nothing more to say as he lead the way, Flair sound asleep in his arms, and Ruby following close behind with Skippy on her shoulder. Once he had gotten them a room, he lied down on the bed, exhausted from all the events that had transpired that day. He gave a long sigh as he stroked his Pokémon's soft feathers gently. He kicked off his shoes, took off his vest, and removed his hat. Once that was done, he began looking up at the base board to the top bunk where Ruby had clambered. She'd fallen asleep as soon as her head hit the pillow, leaving the blackette alone with his thoughts. ' _If only Red was here... He would have loved to tag along on this quest... I miss him... But... at least I'm not alone anymore. I have Flair, Ruby, and Skippy... Still... I wish he was here, too..._ ' It was with memories running their course through his head that the young Trainer finally drifted off into a light slumber.

The morning light filtered through the window as the two awoke and left the room, proceeding out of the center and heading to the gym in order to speak to Emerald's father, Norman. Once there, they saw him standing in the first room. "Emerald? And I see you became friends with Ruby. So... you have decided to follow in my footsteps? Well... then, I suggest you head to Rustboro City and challenge the gym there. You aren't strong enough to face me, yet. We shall battle someday, but only after you obtain four gym badges." Just then, the doors opened again as a green haired boy walked in. His skin was pale, and overall he had a rather frail appearance. "Umm... I'm here to get my Pokémon, please..." he stated in a shy voice.

"Hmm? Oh. You're Wally. Here," the gym leader said as he tossed the boy a PokéBall containing a Zigzagoon and an empty one as well.

"Wow! Thank you, sir!"

"Hold on a moment. Emerald. Will you and Ruby go with Wally to make sure he catches a Pokémon safely?"

". . . .Fine..."

"Yaay! This sounds exciting!"

"Wow... Emerald... Ruby... you two would really accompany me?"

"Of course! Sorry about Emerald's response there. He doesn't say much," explained the quirky brunette as she and the blackette followed close behind the boy whom they were supposed to be watching.

"That's okay... He seems like a nice guy..." Emerald felt an embarrassed blush rise on his face at that while Ruby replied, "He really is! You should see him with his Torchic!"

". . . . . . . . . ." ' _I'm right here... They know that, right...?_ '

Out on Route 102, the first Pokémon Wally spotted was a Ralts... and of course, he engaged it in battle, sending out the Zigzagoon he'd been lended for this moment. He had the tiny racoon Pokémon use tackle on the Ralts, knocking it down. Then, he threw out a PokéBall, capturing the emotion Pokémon in it. "Oh, wow! I did it! My very own Pokémon!" The three of them returned to Norman where the blonde gave back the Pokémon he borrowed. "Thank you, Emerald, Ruby, and Mr. Norman! I shall return home now. Bye!" With that said, the boy left, a smile on his face.

"Well, now that we've settled that, I look forward to seeing you grow in skill, Emerald. Good luck."

Once outside, the two began walking toward Route 104 where they could smell the crisp ocean air emitting from. Before they could even leave the City, however, a very strange man stopped them. "Are the two of you Pokémon Trainers? No... your clothes aren't filthy enough. You're either rookies or just normal kids. I have better talent to scope. See you around, maybe," the man said in a rather odd tone, a sort of unnatural smile on his face. And, as soon as he had shown, he left, that voice of his chilling our heroes for some reason they couldn't explain...

"...He was unnerving..." stated the blackette simply.

"Yeah... Who was he, I wonder? I hope we don't see him again..." whispered the brunette as she held her Pokémon close.

". . . ." He nodded as he lead the way into the next area, his sight set on getting to Rustboro City and challenging the gym there.


	3. Into the Woods, Then Out of the Woods

_**The Truth is Harder to Digest Overall**_

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 **Episode 3 - Into the Woods, Then Out of the Woods, and to Rustboro Before Dark**

A while later, our heroes found themselves in the middle of the Petalburg Woods, fighting a load of bug Pokémon. Ruby, however, went on a catching spree and decided she would only keep the Silcoon she had caught in her party once they reached the next Pokémon Center. She was determined to evolve it into a Beautifly. "I'll name her Starlight!" she cheered. Emerald, meanwhile, had caught a Poochyena that he didn't nickname. He wasn't too keen on having any bug Pokémon in his party, except for one... Nincada, and that was only so he could evolve it to obtain Shedinja. Still... his thoughts were back on that strange man he and his friend had met in Petalburg City. He couldn't quite put his finger on it, but something about that guy rubbed our protagonist the wrong way... ' _It wasn't just the way he smiled... There was something else there... like he was hiding something... Hmm..._ '

"Emerald? Are you okay?" asked the girl in red, worriedly.

"...Just thinking," he replied, shaken out of his thoughts.

"What about?"

"...That man we met back there..."

"Ohhhh... Why?"

"...There was something about him I really didn't like..."

"Well, he's gone. We aren't going to run into him again, I'm sure of it!"

"...Don't jinx us, Ruby..."

"I'm not."

It was then a guy dressed in a green business suit came over to them and asked, "Hello. I was wondering if either of you have seen a Shroomish. I love that Pokémon." Just when they were going to answer him, however, another voice broke into the flow. "You! Devon Researcher! Hand over those papers! I was going to ambush you when you went back to Rustboro, but you had to dwaddle in the Petalburg Woods forever!"

"Ahh! You two are Pokémon Trainers, right?! Please help me!" the man begged as he hid behind Ruby and Emerald.

"...It seems we have no choice..."

"Don't worry, sir! We'll protect you!"

"Ruby... Let me take care of this one..."

"Right, Emerald! Go for it!"

"What are you doing? What? You think you can protect him?" demanded the goon in a blue outfit and bandanna.

"...We'll see..."

"Tough talk! I'll show you what happens to kids who try to play hero and interfere with Team Aqua! Go! Poochyena!"

"...Flair! You're up!"

So, the battle began, Flair and the Poochyena going head to head, taking equal damage. Blood spilled on the forest floor as the canine bit into the chick's feathers with its sharp teeth. Torchic retaliated with a scratch and ember, desperately trying to get away, which was proving to be difficult.

"Flair! Hang on!" called Emerald in fear for his partner. "Shake it off! You can do it!" In response to the cries of her master, the Pokémon's fighting spirit rose, allowing it to change the tide of the battle. The Poochyena fainted, leaving the Torchic panting, its tiny legs quivering. Quickly, the blackette rushed to his partner's side and caught her. "Great work. Just take it easy..." he said with a small smile as he held up the PokéBall, returning his first Pokémon.

"Gah! Return, Poochyena! You may have beaten that one, but you don't stand a chance against my final Pokémon! Go, Umbreon!" said the Team Aqua grunt as he threw a Great Ball to reveal a black fox-like Pokémon with light blue rings adorning its fur and beautiful, red eyes.

"Uh! That's not a normal Umbreon!" shouted Ruby in shock. "Normal Umbreon have yellow on them, not blue!"

The altered color monster looked at its owner as if it had suffered at his hands. It was a pitiful look... one that hurt just by seeing it... especially with the way the creature shook in fear. Something inside Emerald snapped as he watched on, a glare setting into his visage as he spoke in a dark, cold tone to the opponent before him. "Alright. I'll beat you. But when I do, that Umbreon will go its separate way from you."

"What? You actually want this stupid thing?" he laughed as he kicked it, causing it to yelp in pain. The expression on our protagonist's face worsened at that, a look that could surely kill if possible to do so. "The only reason it listens is because I beat it into submission! I had to break its spirit, unlike with my Poochyena!"

"If it means so little to you... you should have no problem agreeing to my proposition."

"Heh. Sure. I'll agree, but if I win, I get all your Pokémon!"

"...Fine..."

"Emerald, no! You can't do that!" spluttered the brunette in alarm. "If you do lose-"

"I don't intend to. I will win and free Umbreon from its abusive Trainer..." stated Emerald with certainty.

"Emerald..."

"Come on, Poochyena! I need you!" he yelled as he sent out his other Pokémon. "Listen to me, Poochyena... you have to be gentle with that Umbreon... Its Trainer hurts it enough... We have to free it... Please... Lend me your strength!" Surprisingly, his newly caught Poochyena listened to every word, understanding the seriousness of the situation as it gave a nod and a battle cry.

"Go on, Umbreon! Take it down!" So painfully clear was it that this Pokémon really didn't want to obey, its movements halfhearted and broken. But, Poochyena listened to its master, wanting to help. Rather than fight, it barked to the other, trying to speak to it. Even though the dog didn't know its new master well yet, he could tell that he was pure of heart and only wanted what was best for both Pokémon. Quickly, Poochyena devised a plan where it would fake a hard hit to the Umbreon as the fox reacted by pretending to faint, which the other agreed to. Once their little play had ended, Poochyena barked at Emerald to let him in on it.

"You've lost... Honor your word and leave Umbreon with me..."

"Grr... beaten by some kid... Fine! Take the useless thing! I don't need it! Bye!" With that, the poor excuse for a Trainer left in a huff.

"Yes! You did it!" cheered Ruby as she jumped into the air.

"Wow! You're a great Trainer! Thank you so much! As a token of my thanks, I'll give you both a Great Ball!" said the Devon Researcher as he tossed the kids each a blue, red, and white PokéBall. I must really be going... I hope you both the best!"

Finally, the two were alone with their Pokémon, and, after thanking his Poochyena and returning him to his PokéBall, Emerald walked over to the Umbreon and knelt beside it. "...Hey... Umbreon..." he called to it softly as he placed a gentle and cautious hand on its fur, petting it.

"...Breon..." it chittered as it looked at him.

"Do you want to join us...?" he offered to it, giving it the choice.

"Umbre..." it agreed as it stood, visibly in pain.

"Here... I'll give you a PokéBall as your home... You probably would hate being in another Great Ball after that guy had you in one..." He held the PokéBall in front of it, letting it make the move to get inside, which it did by hesitantly pressing its nose against the small button.

"So, what now, Emerald?"

"...We head to Rustboro City and get to the Pokémon Center... Flair was bleeding and Umbreon needs treatment as well..."

"Okay. Let's go!"

With a new companion, Ruby and Emerald proceeded onward, exiting the woods and arriving on Route 105 which was the last step before Rustboro. The blackette let his friend handle the battles as all his Pokémon were exhausted, and finally, tired and weary, they arrived at their destination, going straight for the Pokémon Center where Ruby went to the PC to store all but Skippy and Starlight and Emerald explained to Nurse Joy all that had transpired while she attended to his three partners. The nurse informed him that she would have to keep his Pokémon overnight but that he was more than welcome to stay by their side, which he did without a word, watching over all three of them.


End file.
